Comparative Genomics, 7.5 credits

Contents

The course covers central concepts in comparative genomics, including genome assembly, annotation, whole-genome comparisons, phylogenomics and pangenomics. Students are introduced to methods for analysing sequencing data, identifying evolutionary relationships and exploring variation within and between species. Emphasis is placed on understanding and applying bioinformatics workflows for comparative genomics at an advanced level, with focus on biological interpretation and critical analysis.

Expected learning outcomes

After completing the course, the student should be able to:

Knowledge and understanding
1. Explain principles of genome assembly, annotation, phylogenomics and pangenomics.
2. Understand core methods for comparative analyses of genomes and evolutionary processes.

Skills and abilities
3. Apply bioinformatics methods to assemble, annotate and compare genomes.
4. Identify orthology and synteny and analyse evolutionary patterns.
5. Construct and interpret phylogenetic analyses.
6. Build and analyse pangenomes, and present results orally and in writing.

Judgement and approach
7. Critically evaluate genome assemblies, annotations and comparative analyses with respect to quality, reproducibility and biological relevance.

Required Knowledge

At least 60 completed higher education credits in biology, biomedicine, molecular biology, molecular ecology, molecular evolution, genetics or related fields are required. Of these, at least 7.5 credits must be in bioinformatics and 15 credits in molecular biology/molecular ecology/molecular evolution, 7.5 credits in biochemistry/chemistry/mathematics/statistics, 7.5 credits in genetics, and 15 credits at second-cycle level in bioinformatics or related fields. English 6 or equivalent.

Form of instruction

Teaching consists of lectures, supervised computer practicals and project work. Instruction is normally given in English but may be provided in Swedish if there is no need for English. Each student must have access to a personal computer with internet connectivity and the ability to install required software.

Examination modes

Assessment consists of written assignments, an oral presentation and an individual project. The course is graded U (Fail), G (Pass) or VG (Pass with Distinction). To pass the course, all assessed components must be passed; the course grade is determined by the grade on the individual project.
Students who fail an assessment are entitled to a re-examination. The first re-exam must be offered within two months after the original examination, but not earlier than ten working days after results are announced. For examinations conducted in May or June, the first re-exam may be offered within three months after the original examination. At least one additional re-exam must be offered within one year. A student who has passed an assessment may not retake it to obtain a higher grade.
A student who has failed an assessment twice is entitled to request a different examiner, unless special reasons oppose it (Higher Education Ordinance, Chapter 6, Section 22). Requests should be submitted to the Head of the Department of Plant Physiology. The examiner may decide on deviations from the assessment format. Individual adaptation must be considered based on the student’s needs and within the expected learning outcomes. A student with an approved decision on support due to a disability must request adapted assessment no later than ten working days before the examination.

Transitional provisions

If the syllabus ceases to apply or undergoes major changes, students are guaranteed at least three examination opportunities (including the regular examination) according to the syllabus under which they were originally registered, for up to two years after the previous syllabus ceased to apply.